Nick-directed repair of palindromic loop mismatches in human cell extracts

Palindromic sequences present in DNA may form secondary structures that block DNA replication and transcription causing adverse effects on genome stability. It has been suggested that hairpin structures containing mispaired bases could stimulate the repair systems in human cells. In this study, processing of variable length of palindromic loops in the presence or absence of single-base mismatches was investigated in human cell extracts. Our results showed that hairpin structures were efficiently processed through a nick-directed mechanism. In a similar sequence context, mismatch-containing hairpins have higher repair efficiencies. We also found that shorter hairpins are generally better repaired. A strand break located either 3' or 5' to the loop is sufficient to activate hairpin repair on the nicked strand. The reaction requires Mg(2+), the four dNTPs and hydrolysis of ATP for efficient repair on both palindromic loop insertions and deletions. Correction of each of these heteroduplexes was abolished by aphidicolin but was relatively insensitive to the presence of ddTTP, suggesting involvement of polymerase(s) alpha and/or delta. These findings are most consistent with the nick-directed loop repair pathway being responsible for processing hairpin heterologies in human cells.